Web 1

igraph

library(plotly)

## Loading required package: ggplot2

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

library(igraph)

## 
## Attaching package: 'igraph'

## The following object is masked from 'package:plotly':
## 
##     groups

## The following objects are masked from 'package:stats':
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##     decompose, spectrum

## The following object is masked from 'package:base':
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##     union

library(ggnetwork)

g <- read.table("/Users/daniel/Downloads/small_higgs.edgelist")
g <- graph_from_data_frame(g,directed=T,vertices=NULL)

tiny_g <- induced_subgraph(g,1:10)
plot(tiny_g)

gn <- ggnetwork(tiny_g)
g <- ggplot(gn,aes(x=x,y=y,xend=xend,yend=yend)) + geom_nodes() + geom_edges()
g

gn_1 <- ggnetwork(tiny_g,layout=as_tree())
g <- ggplot(gn_1,aes(x=x,y=y,xend=xend,yend=yend)) + geom_nodes() + geom_edges()
g

L <- layout_as_tree(tiny_g)
rownames(L) <- V(tiny_g)$name
el <- as_edgelist(tiny_g)

edge_to_shape <- function(the_row){
  v0 <- the_row[1]
  v1 <- the_row[2]
  the_shape <- list(
    type="line",
    line=list(color="gray",width=0.3),
    x0 = L[v0,1],
    y0 = L[v0,2],
    x1 = L[v1,1],
    y1 = L[v1,2]
  )
}
the_edges <- apply(el,1,edge_to_shape)

edges <- data.frame(ax=L[el[,1],1])
edges$ay <- L[el[,1],2]
edges$x <- L[el[,2],1]
edges$y <- L[el[,2],2]

fig <- plot_ly(x=L[,1],y=L[,2],text=V(tiny_g)$name)
fig <- fig %>% add_markers()
#fig <- fig %>% layout(shapes=the_edges)
fig <- fig %>% add_annotations(data=edges,
                               x=~x,
                               y=~y,
                               ax=~ax,
                               ay=~ay,
                               text="",
                                xref = "x", yref = "y",
                   axref = "x", ayref = "y",
                               showarrow=T)
fig